Search results

$X-Ray Diffraction Studies of Activation and Relaxation In Fast and Slow Rat Skeletal Muscle$

Title: X-Ray Diffraction Studies of Activation and Relaxation In Fast and Slow Rat Skeletal Muscle
Creator: Gong, Henry M.
Date: 2022
Description: The contractile properties of fast-twitch and slow-twitch skeletal muscles are primarily determined by the myosin isoform content and...
Show moreThe contractile properties of fast-twitch and slow-twitch skeletal muscles are primarily determined by the myosin isoform content and modulated by a variety of sarcomere proteins. X-ray diffraction studies of regulatory mechanisms in muscle contraction have focused predominately on fast- or mixed-fiber muscle with slow muscle being much less studied. Here, we used time-resolved x-ray diffraction to investigate the dynamic behavior of the myofilament proteins in relatively pure slow fiber rat soleus (SOL) and pure fast fiber rat extensor digitorum longus (EDL) muscle during twitch and tetanic contractions at optimal lengths (Lo), 95% Lo, and 90% Lo. Before the delivery of stimulation, reduction in muscle length led to decrease in passive tension. The x-ray reflections upon reduction in length showed no transition in the myosin heads from ordered OFF state, where heads are held close to the thick filament backbone, to disordered ON states, where heads are free to bind to thin filament, in both muscles. When stimulation was delivered to both muscles for twitch contractions at Lo, x-ray signatures indicating the transition of myosin heads to ON states were observed in EDL but not in soleus muscle. During tetanic contractions, changes in the disposition of myosin heads as active tension develops is a cooperative process in EDL muscle whereas in soleus muscle this relationship is less cooperative. Moreover, this high cooperativity was maintained in EDL at all lengths tested here, but cooperativity decreased upon reduction in lengths in soleus. The observed reduced extensibility of the thick filaments in soleus muscles as compared to EDL muscles indicate a molecular basis for this behavior. These data indicate that for the EDL thick filament activation is a cooperative strain-induced mechano-sensing mechanism, whereas for the soleus thick filament xiii activation has a more graded response. Lastly, x-ray data collected at different lengths demonstrated that the effect of length on soleus is more pronounce compared to EDL, particularly noticeable in the thick filament during relaxation phase after stimulation ceased. These observations indicate that soleus is more length-dependent than EDL. These different approaches to thick filament regulation in fast- and slow-twitch muscles may be designed to allow for short duration, strong contractions versus sustained finely controlled contractions, respectively.
Show less

Title: Population dynamics and pathogens of the western bean cutworm (Striacosta albicosta)
Creator: Bunn, Dakota C.
Date: 2022
Description: Understanding an herbivorous pest’s population dynamics is necessary to ensure proper integrated pest management strategies are being...
Show moreUnderstanding an herbivorous pest’s population dynamics is necessary to ensure proper integrated pest management strategies are being developed and used. The western bean cutworm is a pest of both corn and dry beans that is understudied and difficult to manage due to its nocturnal lifestyle, adaptation to current management techniques and a general lack of understanding regarding its population structure. Our studies focused on the effects of host plant and pathogens on western bean cutworm population structure and found that mainly adults which developed on corn are contributing to the next generation of western bean cutworm in Michigan, making corn and dry beans unsuitable as co-refuges in insecticide resistance management strategies.We also found a 100% prevalence of the Nosema sp. in the adult population of western bean cutworm in Michigan. This prevalence, when paired with the consistent crop damage caused annually by the western bean cutworm, which confirms an abundance of cutworms are present, suggests the infection is slow acting and non-lethal to its host. Following sequencing, assembly, and annotation of the Nosema sp. genome, we were unable to provide a reason for the Nosema sp.’s low virulence, however, we were able to confirm the presence of all 6 polar tube proteins. Upon further examination of the Nosema sp. genome we were able to determine that it is a true Nosema with genome size of ~9.57 Mbp (~20% of which are transposable elements), which is within the typical range for this genus.
Show less

Title: Biophysical and Computational Characterization of CinDel Edits of Dystrophin
Creator: Stojkovic, Vladimir
Date: 2022
Description: Duchenne muscular dystrophy (DMD) is a degenerative genetic disease caused by a genetic defect that results in the absence of dystrophin, a...
Show moreDuchenne muscular dystrophy (DMD) is a degenerative genetic disease caused by a genetic defect that results in the absence of dystrophin, a protein with an important stabilizing role in muscle cells. DMD causes progressive muscle degeneration leading to the loss of ambulation, and typically results in death before the third decade of life. Treatments for DMD aim to restore dystrophin expression and typically do so by producing edited or modified dystrophins. The only FDA approved therapy, exon skipping, produces dystrophin edits at exon boundaries but emerging therapeutic approaches like gene replacement therapy and CRISPR-Cas9-based gene editing techniques like CinDel allow for greater flexibility and are not constrained to exon boundary edits. However, understanding of what makes a “good”, functional edit is limited so it is not clear how to make use of this increased flexibility to produce optimal edits which are believed to be necessary for robust treatment. In an effort to improve understanding of the biophysics of these non-exon edits, we have embarked on a mixed experimental and computational study of a set of CinDel edits in the D19-D21 region of the dystrophin central rod domain. First, we have conducted an Alphafold structure prediction-based screen of a subset of possible edits in this region and selected one edit for follow-up characterization. We then compared this computationally-selected edit to three other heuristically designed edits experimentally and computationally by molecular dynamics simulations. We found that the computationally selected edit is significantly more thermodynamically stable than the other edits in the cohort. This edit also generally exhibited more favorable properties in MD simulations across multiple measures such as helicity, STR-junction unwinding and conformational variability.
Show less

Title: Apalutamide Modulates the Expression of Regulatory Genes for Prostate Cancer Cell Invasion and Migration In Vivo and In Vitro
Creator: Qualter, Gina E.
Date: 2022
Description: The next generation antiandrogen, Apalutamide (Apa), improves both overall survival and metastasis-free survival in men with castration...
Show moreThe next generation antiandrogen, Apalutamide (Apa), improves both overall survival and metastasis-free survival in men with castration-resistant prostate cancer (CRPC). In vitro and in vivo studies were performed to characterize the mechanistic effects of Apalutamide on prostate cancer cell proliferation, invasion, and migration, and the expression of genes that regulate these processes. Apalutamide inhibited the proliferation of LNCaP human prostate cancer cells in both the presence and absence of dihydrotestosterone (DHT), and also inhibited LNCaP cell migration/invasion. At the mRNA level (RT-PCR), Apalutamide down-regulated the expression of androgen receptor (AR), c-Myc, MMP-2, MMP-9, DANCR, and lncRNA, and up-regulated TIMP-2 expression. Similar data were obtained for protein expression (western blot). In the in vivo study, male Hi-Myc mice received daily oral administration of Apalutamide beginning at age 8 weeks for 2 months, 3.5 months, or 5 months. Daily oral administration of Apalutamide reduced accessory sex gland weights by over 50% at all three time points, inhibited the progression of prostatic intraepithelial neoplasms (PIN) to cancer, and significantly affected the expression of genes that regulate invasion and migration. However, in vitro findings indicated that resistance to Apalutamide through the emergence of the AR splice variant 7 (AR-V7) following extended treatment is possible and may be reversed following knockdown of AR-V7 gene expression.In summary, these results suggest that while Apalutamide is an effective inhibitor of prostate cancer invasion/migration, further investigation into the mechanism of AR-V7 mediated Apalutamide-resistance and strategies to overcome resistance may be indicated to improve prostate cancer patient outcomes following extended periods of treatment.
Show less

Title: The Detection of Emerging Pathogenic Arcobacter Species In Poultry and Poultry By-Products
Creator: Nguyen, Paul
Date: 2022
Description: Arcobacter species are emerging foodborne pathogens that are associated with human gastrointestinal illness. Typical symptoms of Arcobacter...
Show moreArcobacter species are emerging foodborne pathogens that are associated with human gastrointestinal illness. Typical symptoms of Arcobacter infection that have been reported include diarrhea, abdominal cramps, nausea, vomiting, and in severe cases, bacteremia. Consumption of contaminated food and water is the most common transmission source that leads to human infection. When consumed, pathogenic Arcobacter spp. pass through the stomach and establishes themselves in the host intestinal tract, where they cause gastroenteritis. Currently, there is no standard isolation method to detect pathogenic Arcobacter spp. from food and environment sample matrices. The research detailed in this thesis describes the development of the Nguyen-Restaino-Juárez Arcobacter detection system (NRJ) comprised of a selective enrichment broth and a chromogenic agar plate used to isolate three pathogenic species: Arcobacter butzleri, Arcobacter cryaerophilus, and Arcobacter skirrowii. Results revealed that NRJ yielded 97.8% inclusivity and 100.0% exclusivity when evaluating against select bacterial strains found in foods. Our research group internally validated the novel chromogenic detection system by comparing its efficacy against the modified Houf reference method (HB). Method-performance evaluations determined the NRJ method was significantly more sensitive and specific than modified HB when isolating the three Arcobacter species from ground chicken samples. Furthermore, 16S amplicon sequencing data identified that greater than 97% of bacterial isolates recovered using the NRJ detection system were Arcobacter species. This thesis presents the development and validation of a new gold standard method for isolating these emerging pathogens in food, clinical and environmental sampling.
Show less

Title: Evolution and adaptations to host plants in the beetle genus Diabrotica
Creator: Lata, Dimpal
Date: 2022
Description: Corn rootworms (Diabrotica spp.) are among the most destructive pests impacting agriculture in the U.S and are an emerging model for insect...
Show moreCorn rootworms (Diabrotica spp.) are among the most destructive pests impacting agriculture in the U.S and are an emerging model for insect-plant interactions. We have a limited understanding of the genome-scale level difference between specialist and generalist corn rootworm species and their interaction with their host plants. Genome sizesof several species in the genus Diabrotica and an outgroup were estimated using flow cytometry. Results indicated that there has been a recent expansion in genome size in the common ancestor of the virgifera group leading to Diabrotica barberi, Diabrotica virgifera virgifera, and Diabrotica virgifera zeae. Comparative genomic studies between the fucata and virgifera groups of Diabrotica revealed that repeat elements, mostly miniature inverted-transposable elements (MITEs) and gypsy-like long terminal repeat (LTR) retroelements, contributed to genome size expansion. The initial transcriptional profile in western corn rootworm neonates when fed on different potential host plants demonstrated a strong association between western corn rootworm and maize, which was very distinct from other possible hosts and non-host plants. The results also showed presence of several larval development related transcripts unique to host plants and the presence of several muscle development and stress response related transcripts unique to non-host plants. The effect of the maize defensive metabolite DIMBOA on corn rootworms was studied using a novel plant-free system. The survival of both southern and western corn rootworms was not affected at a low concentration of DIMBOA. However, the concentration above the physiological dose found in plants affected the survival of corn rootworms. DIMBOA had no plant independent effect on these corn rootworms weight gain.
Show less

Title: IDENTIFICATION OF THE RIBOFLAVIN BINDING SITE IN VIBRIO CHOLERAE ION PUMPING NQR COMPLEX
Creator: Lee, Chia-Hsing
Date: 2021
Description: NQR is a six-subunit complex that transfers electrons from NADH to ubiquinone, one of the essential enzymes in the bacterial respiratory chain...
Show moreNQR is a six-subunit complex that transfers electrons from NADH to ubiquinone, one of the essential enzymes in the bacterial respiratory chain of many pathogens such as Vibrio cholerae, Pseudomonas aeruginosa, Chlamydia trachomatis. Its electron transfer path requires three different flavin cofactors to facilitate: FAD, FMN, and riboflavin. The FMN in subunit B (FMNB) brings electrons to riboflavin and then transfers it to the final electron receptor UQ in subunit B, coupled with the Na+ pumping mechanism. NQR has a unique evolutionary history, and one of the pieces of evidence is that NQR has been reported as the only one flavoenzyme that uses riboflavin as its redox cofactor. However, the binding site of riboflavin has not been well understood. To gain insight into the electron transfer at this site in V.cholerae NQR, we generated mutants at the interface of subunits B, D, and E where the possible location of riboflavin is. To characterize these mutants, we assessed NQR properties with different approaches including enzyme kinetics and flavin radical profiling. We found that the mutagenesis surrounding the hydrophobic pocket disrupted the NQR activity, and cause the loss of neutral radical, but did not interfere with the binding affinity between the substrates and NQR. This study will help to understand electron transfer better in NQR and develop the drugs targeting the riboflavin binding site in the future.
Show less

Title: STRUCTURE AND DYNAMICS OF MODIFIED NUCLEOSOMES UNDER EPIGENETIC REGULATION
Creator: Kohestani, Havva
Date: 2022
Description: Epigenetic regulations are critical in inducing heritable phenotype changes in biological systems without alternating their core genetic DNA...
Show moreEpigenetic regulations are critical in inducing heritable phenotype changes in biological systems without alternating their core genetic DNA sequences. In vivo, reversible epigenetic mechanisms engage various molecular structures from RNAs to larger proteins. The present thesis investigates the influence of epigenetic regulatory factors such as histone protein variants and small non-coding RNAs on the dynamics and structure of nucleosome core particles. Our results show that a histone substitution is an efficient tool in increasing or decreasing the exposure of DNA to post-translational modification (PTMs) factors or larger molecular assembly elements. Substitution of canonical H2A with H2A.B alters DNA-dimer interface resulting in increased breathing and accessibility of DNA. Replacement of canonical H3 with CENP-A variant impacts the overall core-DNA dynamics with flexibility of DNA entry/ exit sites and more rigid tetramer structure. Histone substitution also affects the micro to macro level molecular communication in the nucleosome system. The long-range correlated motions are weakened in H2A.B compared to canonical NCP. We observed a reduction in effective long-range DNA-DNA and DNA-core allosteric pathways in CENP-A NCP compared to canonical and Widom NCPs. Non-coding RNAs increase the tendency of the H3 tail histones to interact with DNA and induce the structural changes in the initial ideal B-DNA of NCP. Overall, the interaction of epigenetic regulatory factors in the form of protein or nucleic acids shifts the energetic and structural properties of the original nucleosome system. As a result, the chromatin structure is prepared to generate the proper biological response throughout spermatogenesis, chromosome segregation, or PTMs assembly.
Show less

Title: COMPREHENSIVE ANALYSIS OF EXON SKIPPING EDITS WITHIN DYSTROPHIN D20:24 REGIONS
Creator: Niu, Xin
Date: 2020
Description: Exon skipping is a disease modifying therapy that operates at the RNA level. In this strategy, oligonucleotide analog drugs are used to...
Show moreExon skipping is a disease modifying therapy that operates at the RNA level. In this strategy, oligonucleotide analog drugs are used to specifically mask specific exons and prevent them from being included in the mature mRNA. Exon skipping can also be used to restore protein expression in cases where a genetic frameshift mutation has occurred, and this how it is applied to Duchenne muscular dystrophy, DMD. DMD most commonly arises as a result of large exonic deletions that juxtapose flanking exons of incompatible reading frame, which abolishes dystrophin protein expression. This loss leads to the pathology of the disease, which is severe, causing death generally in the second or third decade of life. Here, the primary aim of exon skipping is to restore the reading frame by skipping an exon adjacent to the patient’s original. While restoring some protein expression is good, how removing some region from the middle of protein affects its structure and function is unclear. Complicating this in this case is that the dystrophin gene is very large, containing 79 exons. Many different underlying deletions are knowns, and exon skipping can be applied in many ways. It has previously been shown that many exon-skip edits result in structural perturbations of varying degrees. Very few studies are focused on the protein biophysical study and it is still basically unclear whether and how such editing can be done to minimize such perturbations. In order to provide the solid evidences which prove the significant variation among those cases (especially for the clinically relevant cases) and better understanding the general principles of “what makes a good edit”, we examine a systematic and comprehensive panel of possible exon edits in a region of the dystrophin protein. The domain D20:24 of dystrophin rod region are selected for its entirety which is separated by hinge region (mostly random coiled structure) and addition of other STRs will not disrupt the structure stability. Also D20:24 regions lie in the Hot Spot region II (HS2) which holds the most number of DMD patients. During the comprehensive scan, we identify for the first time, exon edits that appear to maintain structural stability similar to wild-type protein and those clinically relevant edits. Then we figure out the factors that appear to be correlated with the degree of structural perturbation, such as the number of cooperative protein domains, as well as how the edited exon structure interacts with the protein domain structure. Our study is the first systematic and comprehensive scan for an entire multiple STRs domain. This would help us understand the protein nature of various exon skipping edits and provide useful target for clinical treatment. Also the knowledge we learned may be applied to produce more sophisticated CRISPR edits in the future work.
Show less

Title: AMPLIFICATION AND PURIFICATION OF RECOMBINANT PRO-DEATH BAXΔ2 PROTEINS FOR STRUCTURE ANALYSIS
Creator: Zhou, Yi
Date: 2020
Description: BaxΔ2 is an isoform of the pro-apoptotic Bax family of proteins, which is an important anti-cancer protein. BaxΔ2 behaves differently from...
Show moreBaxΔ2 is an isoform of the pro-apoptotic Bax family of proteins, which is an important anti-cancer protein. BaxΔ2 behaves differently from Baxα to induce apoptosis. The current computationally predicted model of BaxΔ2 is based on known Baxα structure, which is considered biased. Therefore, the elucidation of the BaxΔ2 crystal structure is critical. The goal of this project was to obtain a sufficient amount of purified recombinant Bax∆2 protein for crystallization. We cloned full-length BaxΔ2 fused with a poly-histidine tag on either N-terminus (His-Bax∆2) or C-terminus (Bax∆2-His) into an inducible bacterial expression vector. We found that His-Bax∆2 proteins were expressed better than Bax∆2-His, which totally inhibit host growth. However, the protein concentration of His-Bax∆2 was still too low to be detected by Coomassie blue staining. To increase His-Bax∆2 expression and avoid cytotoxicity, we further tested different bacterial host cells and applied the chaperone system. However, all attempts could not overcome Bax∆2 cytotoxicity and the protein expression levels were not high enough to be feasible for further large-scale purification. The mechanism underlying how Bax∆2 inhibits bacterial growth is still a mystery because Bax∆2 eukaryotic targets (mitochondria and caspases) do not exist in bacteria. Further experiments are required to explore the mechanism of Bax∆2 cytotoxicity in bacteria, so as to finally optimize and elevate the BaxΔ2 protein yields.
Show less

Title: Development of a Model To Investigate Inflammation Using Peripheral Blood Mononucleated Cells
Creator: Geevarghese Alex, Peter
Date: 2023
Description: Our modern culture in our society is facing one of the biggest risks in health which is high-calorie diet-related postprandial inflammation....
Show moreOur modern culture in our society is facing one of the biggest risks in health which is high-calorie diet-related postprandial inflammation. Chronic diseases may be caused if the energy-dense food is the choice meaning if it is uncontrolled, clinical studies have demonstrated this with the body's post-meal inflammatory response. We aimed to find the causes of postprandial inflammation in response to various dietary treatments and provide a model to demonstrate. We aimed to make use of in vivo and in vitro techniques and statistics to create a model. The created model would help us to design specific treatments to minimize inflammation with response to dietary. In addition to figuring out vital dietary additives, the model additionally facilitates the layout of individualized interventions to reduce inflammation, thereby improving long-time period health outcomes. We aim to understand the clinical observations of diet-induced postprandial inflammation on the molecular level. We desire to make contributions to reduce the impact of chronic inflammatory disorders that is associated with postprandial inflammation.
Show less

Title: Computational Genomics of Human-Infecting Microsporidia Species from the Genus Encephalitozoon
Creator: Mascarenhas dos Santos, Anne Caroline
Date: 2023
Description: Microsporidia are obligate intracellular pathogens classified as category B priority pathogens by the National Institute of Allergy and...
Show moreMicrosporidia are obligate intracellular pathogens classified as category B priority pathogens by the National Institute of Allergy and Infectious Diseases (NIAID), a division of the National Institutes of Health (NIH). Microsporidian species from the genus Encephalitozoon infect humans and can cause encephalitis, keratoconjunctivitis or enteric diseases in both immunocompromised and immunocompetent individuals. The main treatment for disseminated microsporidiosis available in the United States is albendazole, an anthelmintic benzimidazole that is also used to treat fungal infections, but species from the Encephalitozoonidae have already shown signs of resistance against this drug. The Encephalitozoonidae harbors highly specialized pathogens with the smallest known eukaryote genomes, with Encephalitozoon cuniculi featuring a genome of only 2.9 Mbp and coding for a proteome of roughly 2,000 proteins. Pathogens are in an everlasting race to quicken their adaptation pace against host defenses. This adaptation is often driven by gene duplication, recombination and/or mutation, and due to the potentially disruptive nature of duplication and recombination processes, many of these evolutions in pathogens are taking place outside conserved genomic loci. As such, genes involved in virulence and drug resistance in pathogens are often localized in the (sub)telomeres rather than in chromosome cores. The small and streamlined nature of microsporidian genomes makes them excellent candidates to investigate the adaptation of pathogens to host defenses, the evolution of their virulence, and the development of their resistance to drugs from a genomic perspective. However, microsporidian genomes are highly divergent at the DNA sequence level and the ones that have been sequenced so far are incomplete and are lacking the telomeres. This high level of sequence divergence hinders standard sequence homology-based functional annotations, blurring our understanding of what these organisms are capable of from a metabolic perspective. The gap in our knowledge of what is encoded in the microsporidia telomeres could lead to an underestimation of their pathogenic capabilities. Therefore, deciphering the functions of unknown proteins in microsporidia genomes and unraveling the content of their telomeres is important to fully assess their potential for adaptability to host defenses and predisposition to drug resistance. Likewise, a better understanding of the genetic diversity in microsporidia will help assess the extent by which host-pathogen interactions are shaping the adaptation of these parasites to humans. As observed in the COVID-19 pandemic, genetic diversity can influence the speed at which pathogens adapt to host defenses and thus can pose a big challenge to disease control. The development of strategies for controlling microsporidiosis outbreaks will likely benefit from the work performed in this thesis. As part of my PhD work, I investigated the virulence and host-adaptation capabilities of human-infecting microsporidia species from the genus Encephalitozoon with computational genomic approaches. This work included: 1) using structural homology to infer the functions of unknown proteins from the microsporidia proteome; 2) sequencing the complete genomes from telomere-to-telomere of three distinct Encephalitozoon spp. (E. cuniculi, E. hellem and E. intestinalis) to determine the genetic makeup of their telomeres and better understand the extent of their diversity; and 3) assessing the intraspecies genetic diversity that exists between Encephalitozoon species.
Show less

Title: Migration of Silver from Silver Zeolite/Low-Density Polyethylene Films into Food Stimulants
Creator: Sayeed, Maryam
Date: 2023
Description: Zeolites are naturally occurring or synthetic crystalline microporous aluminosilicate structures with remarkable catalytic, adsorption, and...
Show moreZeolites are naturally occurring or synthetic crystalline microporous aluminosilicate structures with remarkable catalytic, adsorption, and ion-exchange properties. Their unique framework of pores, channels, and cages with precise dimensions makes them an excellent fit for ion exchange and storage. Silver-exchanged zeolite (Ag/Y) composites may be incorporated into polymer matrices to create antimicrobial packaging materials. The slow release of Ag from nanosilver-enabled polymer nanocomposites (PNCs) may inhibit the growth of bacteria and other pathogens on the film’s surface, improving food quality and reducing food waste. However, the migration of Ag ions from the film into food matrices is of great concern as it could expose humans to high concentrations of a heavy metal from dietary sources. The amount of migration depends on various factors, including the potential form of Ag and its concentration in the film, the film thickness, and the storage conditions.The primary objective of this study is to investigate the effect of the form of Ag bound to the zeolite on the migration behavior of Ag from Ag/Y incorporated low-density polyethylene (LDPE) films. For Ag/Y-incorporated LDPE PNCs with distinct Ag species, the Ag migration into the water and Squirt (a commercial soft drink) was at least four times higher from films containing zeolites exchanged with ionic Ag versus zeolites exchanged with nanoparticulate Ag. Similarly, migration into 9 wt % aqueous Domino sugar (granulated sucrose) solution was seven times higher in the ionic silver-incorporated film than in the nanoparticulate Ag film. This study suggests that it is important to consider the form of Ag in silver-exchanged zeolite while producing packaging materials since the potential form of Ag in the PNCs might significantly affect Ag migration behavior.
Show less

Title: Utility of a Low-Coverage Genome Assembly for Discovery of Genes Associated with Pyrethroid Resistance in Smicronyx Fulvus LeConte
Creator: Markiv, Paulina Patrycja
Date: 2023
Description: Red sunflower seed weevil (RSSW) is a major insect pest of cultivated and wild common sunflowers in the Great Plains of North America. The...
Show moreRed sunflower seed weevil (RSSW) is a major insect pest of cultivated and wild common sunflowers in the Great Plains of North America. The extent of the sunflower damage due to RSSW infestation is too great for the natural sunflower defense mechanisms to protect the agriculture industry from losses. Pyrethroids are the only type of insecticide designated for the control of RSSW; however, instances of pyrethroid insecticide ineffectiveness against RSSW have been annually reported to entomologists at South Dakota State University since 2017. The biological bases of insecticide resistance are unknown but common mechanisms associated with pyrethroid resistance include general detoxification mechanism driven by cytochrome P450s (CYP450s) as well as mutations in the pyrethroid target, voltage-gated sodium channels (VGSCs). The goal of this study was to determine if the computational analysis of a low-coverage genome assembly is sufficient to identify and characterize genes associated with insecticide resistance which could contribute to pest control research efforts. By using a low-coverage genome assembly, RNA-Seq data, and bioinformatic tools, 40 complete and 33 partial gene models coding for CYP450 as well as a partial gene model coding for VGSC have been identified in the genome of RSSW. Twenty-seven mutation sites, previously associated with the pyrethroid resistance in other insects, have been identified in the VGSC gene of RSSW. The low-coverage genome proved to be a sufficient resource for preliminary studies of gene identification which could bring significant knowledge to subsequent research focusing on insecticide resistance and pest control.
Show less

Title: LOW-COVERAGE GENOMES AS AN EFFECTIVE AND ECONOMICAL APPROACH FOR LEPIDOPTERAN MICROSATELLITE ISOLATION
Creator: Liang, Huijia
Date: 2020
Description: This study aimed to verify that whether a low-coverage genome can work as an effective approach to isolate Lepidopteran microsatellites. As...
Show moreThis study aimed to verify that whether a low-coverage genome can work as an effective approach to isolate Lepidopteran microsatellites. As microsatellites are useful tool to study population genetics, and there are many Lepidopteran agriculture pests which can cause huge economic damages every year, additionally, Lepidoptera have abundant similar flanking sequences making it difficult to develop reliable microsatellites. However, there are not enough published genomes of Lepidoptera species. If low-coverage Lepidopteran genomes can be used to isolate reliable microsatellites, the low-coverage genomes would be an effective and economical approach for microsatellites isolation, because low-coverage genome sequencing is much cheaper and less time-consuming than the published genome sequencing.
Show less

repository.iit

Search the repository

Pages

Pages

Enabled Filters

Refine Results

Type

Date

Department

Subject

Creator

Rights